The invention discloses a comprehensive treatment method of shale gas extraction water. The method is characterized by comprising: (1) adjusting the pH value of shale gas extraction water to 2.5-5; (2) performing contacting of the pH value-adjusted material, a catalyst and an oxidant under microwave irradiation, and carrying out a microwave catalysis oxidation reaction; (3) adjusting the pH value of the material obtained through the microwave catalysis oxidation to 7.5-12 so as to obtain a suspension; (4) carrying out solid-liquid separation on the suspension to obtain a supernatant and a solid; and (5) carrying out a microwave pressure reducing treatment on the obtained supernatant, and carrying out a harmless treatment on the solid and the remaining residue obtained through the microwave pressure reducing treatment. With the technical scheme of the present invention, the shale gas extraction water can be efficiently treated, the contents of the chlorine ions and other impurities in the treated extraction water are substantially reduced, the treated extraction water can meet the discharge standard or can be recovered and utilized, and the treatment process is simple and effective.